Source code for galaxy.tool_util.deps.mulled.mulled_build

#!/usr/bin/env python
"""Build a mulled image for specified conda targets.

Examples

Build a mulled image with:

    mulled-build build 'samtools=1.3.1--4,bedtools=2.22'

"""

import json
import logging
import os
import shutil
import stat
import string
import subprocess
import sys
from sys import platform as _platform
from typing import (
    List,
    TYPE_CHECKING,
)

import yaml

from galaxy.tool_util.deps import installable
from galaxy.tool_util.deps.conda_util import (
    best_search_result,
    CondaContext,
)
from galaxy.tool_util.deps.docker_util import command_list as docker_command_list
from galaxy.util import (
    commands,
    download_to_file,
    safe_makedirs,
    shlex_join,
    unicodify,
)
from ._cli import arg_parser
from .util import (
    build_target,
    conda_build_target_str,
    create_repository,
    default_mulled_conda_channels_from_env,
    get_files_from_conda_package,
    PrintProgress,
    quay_repository,
    v1_image_name,
    v2_image_name,
)
from ..conda_compat import MetaData

if TYPE_CHECKING:
    from .util import Target

log = logging.getLogger(__name__)

DIRNAME = os.path.dirname(__file__)
DEFAULT_BASE_IMAGE = os.environ.get("DEFAULT_BASE_IMAGE", "quay.io/bioconda/base-glibc-busybox-bash:latest")
DEFAULT_EXTENDED_BASE_IMAGE = os.environ.get(
    "DEFAULT_EXTENDED_BASE_IMAGE", "quay.io/bioconda/base-glibc-debian-bash:latest"
)
DEFAULT_CHANNELS = default_mulled_conda_channels_from_env() or ["conda-forge", "bioconda"]
DEFAULT_REPOSITORY_TEMPLATE = "quay.io/${namespace}/${image}"
DEFAULT_BINDS = ["build/dist:/usr/local/"]
DEFAULT_WORKING_DIR = "/source/"
IS_OS_X = _platform == "darwin"
INVOLUCRO_VERSION = "1.1.2"
DEST_BASE_IMAGE = os.environ.get("DEST_BASE_IMAGE", None)
CONDA_IMAGE = os.environ.get("CONDA_IMAGE", None)

SINGULARITY_TEMPLATE = """Bootstrap: docker
From: %(base_image)s

%%setup

    echo "Copying conda environment"
    mkdir -p /tmp/conda
    cp -r /data/dist/* /tmp/conda/

%%post
    rm -R /usr/local || true
    mkdir -p /usr/local
    cp -R /tmp/conda/* /usr/local/

%%test
    %(container_test)s
"""


def involucro_link():
    if IS_OS_X:
        url = f"https://github.com/mvdbeek/involucro/releases/download/v{INVOLUCRO_VERSION}/involucro.darwin"
    else:
        url = f"https://github.com/involucro/involucro/releases/download/v{INVOLUCRO_VERSION}/involucro"
    return url


def get_tests(args, pkg_path):
    """Extract test cases given a recipe's meta.yaml file."""
    recipes_dir = args.recipes_dir

    tests = []
    input_dir = os.path.dirname(os.path.join(recipes_dir, pkg_path))
    recipe_meta = MetaData(input_dir)

    tests_commands = recipe_meta.get_value("test/commands")
    tests_imports = recipe_meta.get_value("test/imports")
    requirements = recipe_meta.get_value("requirements/run")

    if tests_imports or tests_commands:
        if tests_commands:
            tests.append(" && ".join(tests_commands))
        if tests_imports and "python" in requirements:
            tests.append(" && ".join(f'python -c "import {imp}"' for imp in tests_imports))
        elif tests_imports and ("perl" in requirements or "perl-threaded" in requirements):
            tests.append(" && ".join(f'''perl -e "use {imp};\"''' for imp in tests_imports))

    tests = " && ".join(tests)
    tests = tests.replace("$R ", "Rscript ")
    return tests


def get_pkg_name(args, pkg_path):
    """Extract the package name from a given meta.yaml file."""
    recipes_dir = args.recipes_dir

    input_dir = os.path.dirname(os.path.join(recipes_dir, pkg_path))
    recipe_meta = MetaData(input_dir)
    return recipe_meta.get_value("package/name")


def get_affected_packages(args):
    """Return a list of all meta.yaml file that where modified/created recently.

    Length of time to check for indicated by the ``hours`` parameter.
    """
    recipes_dir = args.recipes_dir
    hours = args.diff_hours
    cmd = ["git", "log", "--diff-filter=ACMRTUXB", "--name-only", '--pretty=""', f'--since="{hours} hours ago"']
    changed_files = unicodify(subprocess.check_output(cmd, cwd=recipes_dir)).splitlines()
    pkg_list = {x for x in changed_files if x.startswith("recipes/") and x.endswith("meta.yaml")}
    for pkg in pkg_list:
        if pkg and os.path.exists(os.path.join(recipes_dir, pkg)):
            yield (get_pkg_name(args, pkg), get_tests(args, pkg))


def conda_versions(pkg_name, file_name):
    """Return all conda version strings for a specified package name."""
    j = json.load(open(file_name))
    ret = list()
    for pkg in j["packages"].values():
        if pkg["name"] == pkg_name:
            ret.append(f"{pkg['version']}--{pkg['build']}")
    return ret


def get_conda_hits_for_targets(targets, conda_context):
    search_results = (best_search_result(t, conda_context, platform="linux-64")[0] for t in targets)
    return [r for r in search_results if r]


def base_image_for_targets(targets: List["Target"], conda_context: CondaContext) -> str:
    """
    determine base image (DEFAULT_BASE_IMAGE/DEFAULT_EXTENDED_BASE_IMAGE) for a
    list of targets by inspecting the conda package (i.e. if the use of an
    extended image is indicated in info/about.json or info/recipe/meta.yaml
    """
    hits = get_conda_hits_for_targets(targets, conda_context)
    for hit in hits:
        try:
            content_dict = get_files_from_conda_package(hit["url"], ["info/about.json", "info/recipe/meta.yaml"])
            if "info/about.json" in content_dict and json.loads(unicodify(content_dict["info/about.json"])).get(
                "extra", {}
            ).get("container", {}).get("extended-base", False):
                return DEFAULT_EXTENDED_BASE_IMAGE
            elif "info/recipe/meta.yaml" in content_dict and (
                yaml.safe_load(unicodify(content_dict["info/recipe/meta.yaml"]))
                .get("extra", {})
                .get("container", {})
                .get("extended-base", False)
            ):
                return DEFAULT_EXTENDED_BASE_IMAGE
        except Exception:
            log.warning(
                "Could not load metadata.yaml for '%s', version '%s'", hit["name"], hit["version"], exc_info=True
            )
    return DEFAULT_BASE_IMAGE


class BuildExistsException(Exception):
    """Exception indicating mull_targets is skipping an existing build.

    If mull_targets is called with rebuild=False and the target built is already published
    an instance of this exception is thrown.
    """


def mull_targets(
    targets,
    involucro_context=None,
    command="build",
    channels=DEFAULT_CHANNELS,
    namespace="biocontainers",
    test="true",
    test_files=None,
    image_build=None,
    name_override=None,
    repository_template=DEFAULT_REPOSITORY_TEMPLATE,
    dry_run=False,
    conda_version=None,
    mamba_version=None,
    use_mamba=False,
    verbose=False,
    binds=DEFAULT_BINDS,
    rebuild=True,
    oauth_token=None,
    hash_func="v2",
    singularity=False,
    singularity_image_dir="singularity_import",
    base_image=None,
    determine_base_image=True,
):
    targets = list(targets)
    if involucro_context is None:
        involucro_context = InvolucroContext()

    image_function = v1_image_name if hash_func == "v1" else v2_image_name
    if len(targets) > 1 and image_build is None:
        # Force an image build in this case - this seems hacky probably
        # shouldn't work this way but single case broken else wise.
        image_build = "0"

    repo_template_kwds = {
        "namespace": namespace,
        "image": image_function(targets, image_build=image_build, name_override=name_override),
    }
    repo = string.Template(repository_template).safe_substitute(repo_template_kwds)

    if not rebuild or "push" in command:
        repo_name = repo_template_kwds["image"].split(":", 1)[0]
        repo_data = quay_repository(repo_template_kwds["namespace"], repo_name)
        if not rebuild:
            tags = repo_data.get("tags", [])

            target_tag = None
            if ":" in repo_template_kwds["image"]:
                image_name_parts = repo_template_kwds["image"].split(":")
                assert len(image_name_parts) == 2, f": not allowed in image name [{repo_template_kwds['image']}]"
                target_tag = image_name_parts[1]

            if tags and (target_tag is None or target_tag in tags):
                raise BuildExistsException()
        if "push" in command and "error_type" in repo_data and oauth_token:
            # Explicitly create the repository so it can be built as public.
            create_repository(repo_template_kwds["namespace"], repo_name, oauth_token)

    for channel in channels:
        if channel.startswith("file://"):
            bind_path = channel[7:]
            binds.append(f"{bind_path}:{bind_path}")

    channels_str = ",".join(channels)
    target_str = ",".join(map(conda_build_target_str, targets))
    bind_str = ",".join(binds)
    involucro_args = [
        "-f",
        f"{DIRNAME}/invfile.lua",
        "-set",
        f"CHANNELS={channels_str}",
        "-set",
        f"TARGETS={target_str}",
        "-set",
        f"REPO={repo}",
        "-set",
        f"BINDS={bind_str}",
    ]
    dest_base_image = None
    if base_image:
        dest_base_image = base_image
    elif DEST_BASE_IMAGE:
        dest_base_image = DEST_BASE_IMAGE
    elif determine_base_image:
        conda_context = CondaInDockerContext(ensure_channels=channels)
        dest_base_image = base_image_for_targets(targets, conda_context)

    if dest_base_image:
        involucro_args.extend(["-set", f"DEST_BASE_IMAGE={dest_base_image}"])
    if CONDA_IMAGE:
        involucro_args.extend(["-set", f"CONDA_IMAGE={CONDA_IMAGE}"])
    if verbose:
        involucro_args.extend(["-set", "VERBOSE=1"])
    if singularity:
        singularity_image_name = repo_template_kwds["image"]
        involucro_args.extend(["-set", "SINGULARITY=1"])
        involucro_args.extend(["-set", f"SINGULARITY_IMAGE_NAME={singularity_image_name}"])
        involucro_args.extend(["-set", f"SINGULARITY_IMAGE_DIR={singularity_image_dir}"])
        involucro_args.extend(["-set", f"USER_ID={os.getuid()}:{os.getgid()}"])
    if test:
        involucro_args.extend(["-set", f"TEST={test}"])

    verbose = "--verbose" if verbose else "--quiet"
    conda_bin = "conda"
    if use_mamba:
        conda_bin = "mamba"
        if mamba_version is None:
            mamba_version = ""
    involucro_args.extend(["-set", "CONDA_BIN=%s" % conda_bin])
    if conda_version is not None or mamba_version is not None:
        mamba_test = "true"
        specs = []
        if conda_version is not None:
            specs.append(f"conda={conda_version}")
        if mamba_version is not None:
            specs.append(f"mamba={mamba_version}")
            if mamba_version == "" and not specs:
                # If nothing but mamba without a specific version is requested,
                # then only run conda install if mamba is not already installed.
                mamba_test = "[ '[]' = \"$( conda list --json --full-name mamba )\" ]"
        conda_install = f"""conda install {verbose} --yes {" ".join(f"'{spec}'" for spec in specs)}"""
        involucro_args.extend(["-set", f"PREINSTALL=if {mamba_test} ; then {conda_install} ; fi"])

    involucro_args.append(command)
    if test_files:
        test_bind = []
        for test_file in test_files:
            if ":" not in test_file:
                if os.path.exists(test_file):
                    test_bind.append(f"{test_file}:{DEFAULT_WORKING_DIR}/{test_file}")
            else:
                if os.path.exists(test_file.split(":")[0]):
                    test_bind.append(test_file)
        if test_bind:
            involucro_args.insert(6, "-set")
            involucro_args.insert(7, f"TEST_BINDS={','.join(test_bind)}")
    cmd = involucro_context.build_command(involucro_args)
    print(f"Executing: {shlex_join(cmd)}")
    if dry_run:
        return 0
    ensure_installed(involucro_context, True)
    if singularity:
        if not os.path.exists(singularity_image_dir):
            safe_makedirs(singularity_image_dir)
        with open(os.path.join(singularity_image_dir, "Singularity.def"), "w+") as sin_def:
            fill_template = SINGULARITY_TEMPLATE % {
                "container_test": test,
                "base_image": dest_base_image or DEFAULT_BASE_IMAGE,
            }
            sin_def.write(fill_template)
    with PrintProgress():
        ret = involucro_context.exec_command(involucro_args)
    if singularity:
        # we can not remove this folder as it contains the image wich is owned by root
        pass
        # shutil.rmtree('./singularity_import')
    return ret


def context_from_args(args):
    verbose = "2" if not args.verbose else "3"
    return InvolucroContext(involucro_bin=args.involucro_path, verbose=verbose)


class CondaInDockerContext(CondaContext):
    def __init__(
        self,
        conda_prefix=None,
        conda_exec=None,
        shell_exec=None,
        debug=False,
        ensure_channels=DEFAULT_CHANNELS,
        condarc_override=None,
    ):
        if not conda_exec:
            conda_image = CONDA_IMAGE or "continuumio/miniconda3:latest"
            binds = []
            for channel in ensure_channels:
                if channel.startswith("file://"):
                    bind_path = channel[7:]
                    binds.extend(["-v", f"{bind_path}:{bind_path}"])
            conda_exec = docker_command_list("run", binds + [conda_image, "conda"])
        super().__init__(
            conda_prefix=conda_prefix,
            conda_exec=conda_exec,
            shell_exec=shell_exec,
            debug=debug,
            ensure_channels=ensure_channels,
            condarc_override=condarc_override,
        )


class InvolucroContext(installable.InstallableContext):
    installable_description = "Involucro"

    def __init__(self, involucro_bin=None, shell_exec=None, verbose="3"):
        if involucro_bin is None:
            if os.path.exists("./involucro"):
                self.involucro_bin = "./involucro"
            else:
                self.involucro_bin = "involucro"
        else:
            self.involucro_bin = involucro_bin
        self.shell_exec = shell_exec or commands.shell
        self.verbose = verbose

    def build_command(self, involucro_args):
        return [self.involucro_bin, f"-v={self.verbose}"] + involucro_args

    def exec_command(self, involucro_args):
        cmd = self.build_command(involucro_args)
        # Create ./build dir manually, otherwise Docker will do it as root
        created_build_dir = False
        if not os.path.exists("build"):
            created_build_dir = True
            os.mkdir("./build")
        try:
            res = self.shell_exec(cmd)
        finally:
            # delete build directory in any case
            if created_build_dir:
                shutil.rmtree("./build")
        return res

    def is_installed(self):
        return os.path.exists(self.involucro_bin)

    def can_install(self):
        return True

    @property
    def parent_path(self):
        return os.path.dirname(os.path.abspath(self.involucro_bin))


def ensure_installed(involucro_context, auto_init):
    return installable.ensure_installed(involucro_context, install_involucro, auto_init)


def install_involucro(involucro_context):
    install_path = os.path.abspath(involucro_context.involucro_bin)
    involucro_context.involucro_bin = install_path

    try:
        download_to_file(involucro_link(), install_path)
    except Exception:
        log.exception(f"Failed to download involucro from url '{involucro_link()}'")
        return 1
    try:
        os.chmod(install_path, os.stat(install_path).st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
        return 0
    except Exception:
        log.exception("Failed to make file '%s' executable", install_path)
        return 1


def add_build_arguments(parser):
    """Base arguments describing how to 'mull'."""
    parser.add_argument(
        "--involucro-path",
        dest="involucro_path",
        default=None,
        help="Path to involucro (if not set will look in working directory and on PATH).",
    )
    parser.add_argument(
        "--dry-run", dest="dry_run", action="store_true", help="Just print commands instead of executing them."
    )
    parser.add_argument("--verbose", dest="verbose", action="store_true", help="Cause process to be verbose.")
    parser.add_argument("--singularity", action="store_true", help="Additionally build a singularity image.")
    parser.add_argument(
        "--singularity-image-dir", dest="singularity_image_dir", help="Directory to write singularity images too."
    )
    parser.add_argument("-n", "--namespace", dest="namespace", default="biocontainers", help="quay.io namespace.")
    parser.add_argument(
        "-r",
        "--repository_template",
        dest="repository_template",
        default=DEFAULT_REPOSITORY_TEMPLATE,
        help="Docker repository target for publication (only quay.io or compat. API is currently supported).",
    )
    parser.add_argument(
        "-c",
        "--channels",
        dest="channels",
        default=",".join(DEFAULT_CHANNELS),
        help="Comma separated list of target conda channels.",
    )
    parser.add_argument(
        "--conda-version",
        dest="conda_version",
        default=None,
        help="Change to specified version of Conda before installing packages.",
    )
    parser.add_argument(
        "--mamba-version",
        dest="mamba_version",
        default=None,
        help="Change to specified version of Mamba before installing packages.",
    )
    parser.add_argument(
        "--use-mamba",
        dest="use_mamba",
        action="store_true",
        help="Use Mamba instead of Conda for package installation.",
    )
    parser.add_argument(
        "--oauth-token",
        dest="oauth_token",
        default=None,
        help="If set, use this token when communicating with quay.io API.",
    )
    parser.add_argument("--check-published", dest="rebuild", action="store_false")
    parser.add_argument("--hash", dest="hash", choices=["v1", "v2"], default="v2")


def add_single_image_arguments(parser):
    parser.add_argument(
        "--name-override",
        dest="name_override",
        default=None,
        help="Override mulled image name - this is not recommended since metadata will not be detectable from the name of resulting images",
    )
    parser.add_argument(
        "--image-build", dest="image_build", default=None, help="Build a versioned variant of this image."
    )


def target_str_to_targets(targets_raw):
    def parse_target(target_str):
        if "=" in target_str:
            package_name, version = target_str.split("=", 1)
            build = None
            if "=" in version:
                version, build = version.split("=")
            elif "--" in version:
                version, build = version.split("--")
            target = build_target(package_name, version, build)
        else:
            target = build_target(target_str)
        return target

    targets = [parse_target(_) for _ in targets_raw.split(",")]
    return targets


def args_to_mull_targets_kwds(args):
    kwds = {}
    if hasattr(args, "image_build"):
        kwds["image_build"] = args.image_build
    if hasattr(args, "name_override"):
        kwds["name_override"] = args.name_override
    if hasattr(args, "namespace"):
        kwds["namespace"] = args.namespace
    if hasattr(args, "dry_run"):
        kwds["dry_run"] = args.dry_run
    if hasattr(args, "singularity"):
        kwds["singularity"] = args.singularity
    if hasattr(args, "test"):
        kwds["test"] = args.test
    if hasattr(args, "test_files"):
        if args.test_files:
            kwds["test_files"] = args.test_files.split(",")
    if hasattr(args, "channels"):
        kwds["channels"] = args.channels.split(",")
    if hasattr(args, "command"):
        kwds["command"] = args.command
    if hasattr(args, "repository_template"):
        kwds["repository_template"] = args.repository_template
    if hasattr(args, "conda_version"):
        kwds["conda_version"] = args.conda_version
    if hasattr(args, "mamba_version"):
        kwds["mamba_version"] = args.mamba_version
    if hasattr(args, "use_mamba"):
        kwds["use_mamba"] = args.use_mamba
    if hasattr(args, "oauth_token"):
        kwds["oauth_token"] = args.oauth_token
    if hasattr(args, "rebuild"):
        kwds["rebuild"] = args.rebuild
    if hasattr(args, "hash"):
        kwds["hash_func"] = args.hash
    if hasattr(args, "singularity_image_dir") and args.singularity_image_dir:
        kwds["singularity_image_dir"] = args.singularity_image_dir

    kwds["involucro_context"] = context_from_args(args)

    return kwds


[docs]def main(argv=None):
    """Main entry-point for the CLI tool."""
    parser = arg_parser(argv, globals())
    add_build_arguments(parser)
    add_single_image_arguments(parser)
    parser.add_argument("command", metavar="COMMAND", help="Command (build-and-test, build, all)")
    parser.add_argument(
        "targets", metavar="TARGETS", default=None, help="Build a single container with specific package(s)."
    )
    parser.add_argument(
        "--repository-name",
        dest="repository_name",
        default=None,
        help="Name of mulled container (leave blank to auto-generate based on packages - recommended).",
    )
    parser.add_argument("--test", help="Provide a test command for the container.")
    parser.add_argument(
        "--test-files",
        help="Provide test-files that may be required to run the test command. Individual mounts are separated by comma."
        "The source:dest docker syntax is respected. If relative file paths are given, files will be mounted in /source/<relative_file_path>",
    )
    args = parser.parse_args()
    targets = target_str_to_targets(args.targets)
    sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args)))


__all__ = (
    "main",
    "build_target",
)


if __name__ == "__main__":
    main()