Source code for galaxy.jobs.command_factory

from logging import getLogger
from os import getcwd
from os.path import (
    abspath,
    join
)

from galaxy import util
from galaxy.jobs.runners.util.job_script import (
    check_script_integrity,
    INTEGRITY_INJECTION,
    write_script,
)

log = getLogger(__name__)

CAPTURE_RETURN_CODE = "return_code=$?"
YIELD_CAPTURED_CODE = 'sh -c "exit $return_code"'
SETUP_GALAXY_FOR_METADATA = """
[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
"""
PREPARE_DIRS = """mkdir -p working outputs configs
if [ -d _working ]; then
    rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs
else
    cp -R working _working; cp -R outputs _outputs; cp -R configs _configs
fi
cd working"""


[docs]def build_command(
    runner,
    job_wrapper,
    container=None,
    modify_command_for_container=True,
    include_metadata=False,
    include_work_dir_outputs=True,
    create_tool_working_directory=True,
    remote_command_params={},
    remote_job_directory=None,
    stdout_file=None,
    stderr_file=None,
):
    """
    Compose the sequence of commands necessary to execute a job. This will
    currently include:

        - environment settings corresponding to any requirement tags
        - preparing input files
        - command line taken from job wrapper
        - commands to set metadata (if include_metadata is True)
    """
    shell = job_wrapper.shell
    base_command_line = job_wrapper.get_command_line()
    # job_id = job_wrapper.job_id
    # log.debug( 'Tool evaluation for job (%s) produced command-line: %s' % ( job_id, base_command_line ) )
    if not base_command_line:
        raise Exception("Attempting to run a tool with empty command definition.")

    commands_builder = CommandsBuilder(base_command_line)

    # All job runners currently handle this case which should never occur
    if not commands_builder.commands:
        return None

    # Version, dependency resolution, and task splitting are prepended to the
    # command - so they need to appear in the following order to ensure that
    # the underlying application used by version command is available in the
    # environment after dependency resolution, but the task splitting command
    # is still executed in Galaxy's Python environment.

    __handle_version_command(commands_builder, job_wrapper)

    # One could imagine also allowing dependencies inside of the container but
    # that is too sophisticated for a first crack at this - build your
    # containers ready to go!
    if not container or container.resolve_dependencies:
        __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)

    __handle_task_splitting(commands_builder, job_wrapper)

    if (container and modify_command_for_container) or job_wrapper.commands_in_new_shell:
        if container and modify_command_for_container:
            # Many Docker containers do not have /bin/bash.
            external_command_shell = container.shell
        else:
            external_command_shell = shell
        externalized_commands = __externalize_commands(job_wrapper, external_command_shell, commands_builder, remote_command_params, container=container)
        if container and modify_command_for_container:
            # Stop now and build command before handling metadata and copying
            # working directory files back. These should always happen outside
            # of docker container - no security implications when generating
            # metadata and means no need for Galaxy to be available to container
            # and not copying workdir outputs back means on can be more restrictive
            # of where container can write to in some circumstances.
            run_in_container_command = container.containerize_command(
                externalized_commands
            )
            commands_builder = CommandsBuilder(run_in_container_command)
        else:
            commands_builder = CommandsBuilder(externalized_commands)

    # Don't need to create a separate tool working directory for Pulsar
    # jobs - that is handled by Pulsar.
    if create_tool_working_directory:
        # usually working will already exist, but it will not for task
        # split jobs.

        # Copy working and outputs before job submission so that these can be restored on resubmission
        # xref https://github.com/galaxyproject/galaxy/issues/3289
        commands_builder.prepend_command(PREPARE_DIRS)

    container_monitor_command = job_wrapper.container_monitor_command(container)
    if container_monitor_command:
        commands_builder.prepend_command(container_monitor_command)

    if include_work_dir_outputs:
        __handle_work_dir_outputs(commands_builder, job_wrapper, runner, remote_command_params)

    if stdout_file and stderr_file:
        commands_builder.capture_stdout_stderr(stdout_file, stderr_file)
    commands_builder.capture_return_code()

    if include_metadata and job_wrapper.requires_setting_metadata:
        working_directory = remote_job_directory or job_wrapper.working_directory
        commands_builder.append_command("cd '%s'" % working_directory)
        __handle_metadata(commands_builder, job_wrapper, runner, remote_command_params)

    return commands_builder.build()


def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_params, script_name="tool_script.sh", container=None):
    local_container_script = join(job_wrapper.working_directory, script_name)
    tool_commands = commands_builder.build()
    config = job_wrapper.app.config
    integrity_injection = ""
    # Setting shell to none in job_conf.xml disables creating a tool command script,
    # set -e doesn't work for composite commands but this is necessary for Windows jobs
    # for instance.
    if shell and shell.lower() == 'none':
        return tool_commands
    if check_script_integrity(config):
        integrity_injection = INTEGRITY_INJECTION
    set_e = ""
    if job_wrapper.strict_shell:
        set_e = "set -e\n"
    source_command = ""
    if container:
        source_command = container.source_environment
    script_contents = "#!{}\n{}{}{}{}".format(
        shell,
        integrity_injection,
        set_e,
        source_command,
        tool_commands,
    )
    write_script(local_container_script, script_contents, config)
    commands = "{} {}".format(shell, local_container_script)
    # TODO: Cleanup for_pulsar hack.
    # - Integrate Pulsar sending tool_stdout/tool_stderr back
    #   https://github.com/galaxyproject/pulsar/pull/202
    # *and*
    # - Get Galaxy to write these files to an output directory so the container itself
    #   doesn't need to mount the job directory (rw) and then eliminate this hack
    #   (or restrict to older Pulsar versions).
    #   https://github.com/galaxyproject/galaxy/pull/8449
    for_pulsar = False
    if 'script_directory' in remote_command_params:
        commands = "{} {}".format(shell, join(remote_command_params['script_directory'], script_name))
        for_pulsar = True
    if not for_pulsar:
        commands += " > ../outputs/tool_stdout 2> ../outputs/tool_stderr"
    log.info("Built script [{}] for tool command [{}]".format(local_container_script, tool_commands))
    return commands


def __handle_version_command(commands_builder, job_wrapper):
    # Prepend version string
    write_version_cmd = job_wrapper.write_version_cmd
    if write_version_cmd:
        commands_builder.prepend_command(write_version_cmd)


def __handle_task_splitting(commands_builder, job_wrapper):
    # prepend getting input files (if defined)
    if getattr(job_wrapper, 'prepare_input_files_cmds', None):
        commands_builder.prepend_commands(job_wrapper.prepare_input_files_cmds)


def __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params):
    local_dependency_resolution = remote_command_params.get("dependency_resolution", "local") == "local"
    # Prepend dependency injection
    if local_dependency_resolution and job_wrapper.dependency_shell_commands:
        commands_builder.prepend_commands(job_wrapper.dependency_shell_commands)


def __handle_work_dir_outputs(commands_builder, job_wrapper, runner, remote_command_params):
    # Append commands to copy job outputs based on from_work_dir attribute.
    work_dir_outputs_kwds = {}
    if 'working_directory' in remote_command_params:
        work_dir_outputs_kwds['job_working_directory'] = remote_command_params['working_directory']
    work_dir_outputs = runner.get_work_dir_outputs(job_wrapper, **work_dir_outputs_kwds)
    if work_dir_outputs:
        commands_builder.capture_return_code()
        copy_commands = map(__copy_if_exists_command, work_dir_outputs)
        commands_builder.append_commands(copy_commands)


def __handle_metadata(commands_builder, job_wrapper, runner, remote_command_params):
    # Append metadata setting commands, we don't want to overwrite metadata
    # that was copied over in init_meta(), as per established behavior
    metadata_kwds = remote_command_params.get('metadata_kwds', {})
    exec_dir = metadata_kwds.get('exec_dir', abspath(getcwd()))
    tmp_dir = metadata_kwds.get('tmp_dir', job_wrapper.working_directory)
    dataset_files_path = metadata_kwds.get('dataset_files_path', runner.app.model.Dataset.file_path)
    output_fnames = metadata_kwds.get('output_fnames', job_wrapper.get_output_fnames())
    config_root = metadata_kwds.get('config_root', None)
    config_file = metadata_kwds.get('config_file', None)
    datatypes_config = metadata_kwds.get('datatypes_config', None)
    compute_tmp_dir = metadata_kwds.get('compute_tmp_dir', None)
    resolve_metadata_dependencies = job_wrapper.commands_in_new_shell
    metadata_command = job_wrapper.setup_external_metadata(
        exec_dir=exec_dir,
        tmp_dir=tmp_dir,
        dataset_files_path=dataset_files_path,
        output_fnames=output_fnames,
        set_extension=False,
        config_root=config_root,
        config_file=config_file,
        datatypes_config=datatypes_config,
        compute_tmp_dir=compute_tmp_dir,
        resolve_metadata_dependencies=resolve_metadata_dependencies,
        use_bin=job_wrapper.use_metadata_binary,
        kwds={'overwrite': False}
    ) or ''
    metadata_command = metadata_command.strip()
    if metadata_command:
        # Place Galaxy and its dependencies in environment for metadata regardless of tool.
        metadata_command = "{}{}".format(SETUP_GALAXY_FOR_METADATA, metadata_command)
        commands_builder.capture_return_code()
        commands_builder.append_command(metadata_command)


def __copy_if_exists_command(work_dir_output):
    source_file, destination = work_dir_output
    return "if [ -f {} ] ; then cp {} {} ; fi".format(source_file, source_file, destination)


class CommandsBuilder:

    def __init__(self, initial_command=''):
        # Remove trailing semi-colon so we can start hacking up this command.
        # TODO: Refactor to compose a list and join with ';', would be more clean.
        initial_command = util.unicodify(initial_command)
        commands = initial_command.rstrip("; ")
        self.commands = commands

        # Coping work dir outputs or setting metadata will mask return code of
        # tool command. If these are used capture the return code and ensure
        # the last thing that happens is an exit with return code.
        self.return_code_captured = False

    def prepend_command(self, command, sep=";"):
        if command:
            self.commands = "{}{} {}".format(command,
                                         sep,
                                         self.commands)
        return self

    def prepend_commands(self, commands):
        return self.prepend_command("; ".join(c for c in commands if c))

    def append_command(self, command, sep=';'):
        if command:
            self.commands = "{}{} {}".format(self.commands,
                                          sep,
                                          command)
        return self

    def append_commands(self, commands):
        self.append_command("; ".join(c for c in commands if c))

    def capture_stdout_stderr(self, stdout_file, stderr_file):
        self.prepend_command("""out="${TMPDIR:-/tmp}/out.$$" err="${TMPDIR:-/tmp}/err.$$"
mkfifo "$out" "$err"
trap 'rm "$out" "$err"' EXIT
tee -a stdout.log < "$out" &
tee -a stderr.log < "$err" >&2 &""",
                             sep="")
        self.append_command("> '{stdout_file}' 2> '{stderr_file}'".format(stdout_file=stdout_file,
                                                                          stderr_file=stderr_file),
                            sep="")

    def capture_return_code(self):
        if not self.return_code_captured:
            self.return_code_captured = True
            self.append_command(CAPTURE_RETURN_CODE)

    def build(self):
        if self.return_code_captured:
            self.append_command(YIELD_CAPTURED_CODE)
        return self.commands


__all__ = ("build_command", )