comparison env/lib/python3.9/site-packages/planemo/commands/cmd_container_register.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

0:4f3585e2f14b

"""Module describing the planemo ``container_register`` command."""
import os
import string

import click
from galaxy.tool_util.deps.container_resolvers.mulled import targets_to_mulled_name
from galaxy.tool_util.deps.mulled.mulled_build import (
    base_image_for_targets,
    DEFAULT_BASE_IMAGE,
)
from galaxy.tool_util.deps.mulled.util import (
    conda_build_target_str,
    v2_image_name,
)

from planemo import options
from planemo.cli import command_function
from planemo.conda import (
    best_practice_search,
    build_conda_context,
    collect_conda_target_lists_and_tool_paths
)
from planemo.git import add, branch, commit, push
from planemo.github_util import (
    clone_fork_branch,
    DEFAULT_REMOTE_NAME,
    get_repository_object,
    pull_request,
)
from planemo.mulled import conda_to_mulled_targets

REGISTRY_TARGET_NAME = "multi-package-containers"
REGISTRY_TARGET_PATH = "combinations"
REGISTRY_REPOSITORY = "BioContainers/multi-package-containers"
DEFAULT_MESSAGE = "Add container $hash.\n**Hash**: $hash\n\n**Packages**:\n$packages\nBase Image:$base_image\n\n"
DEFAULT_MESSAGE += "**For** :\n$tools\n\nGenerated with Planemo."
CONTENTS = "#targets\tbase_image\timage_build\n$targets\t$base_image\t$image_build\n"
BIOCONTAINERS_PLATFORM = 'linux-64'


@click.command('container_register')
@options.optional_tools_arg(multiple=True)
@options.recursive_option()
@options.mulled_namespace_option()
@options.conda_target_options()
@click.option(
    "output_directory",
    "--output_directory",
    type=click.Path(
        file_okay=False,
        dir_okay=True,
        resolve_path=True,
    ),
    default=None,
    help=("Container registration directory (defaults to ~/.planemo/multi-package-containers."),
)
@click.option(
    "-m",
    "--message",
    default=DEFAULT_MESSAGE,
    help="Commit and pull request message template for registration interactions."
)
@click.option(
    "--pull_request/--no_pull_request",
    is_flag=True,
    default=True,
    help="Fork and create a pull request against %s for these changes." % REGISTRY_REPOSITORY
)
@click.option(
    "--force_push/--no_force_push",
    is_flag=True,
    default=False,
    help="Force push branch for pull request in case it already exists.",
)
@command_function
def cli(ctx, paths, **kwds):
    """Register multi-requirement containers as needed.

    BioContainers publishes all Bioconda packages automatically as individual
    container images. These however are not enough for tools with multiple
    best-practice requirements. Such requirements should be recorded and published
    so that a container can be created and registered for these tools.
    """
    registry_target = RegistryTarget(ctx, **kwds)
    conda_context = build_conda_context(ctx, **kwds)

    combinations_added = 0
    conda_targets_list, tool_paths_list = collect_conda_target_lists_and_tool_paths(ctx, paths, recursive=kwds["recursive"])
    for conda_targets, tool_paths in zip(conda_targets_list, tool_paths_list):
        ctx.vlog("Handling conda_targets [%s]" % conda_targets)
        mulled_targets = conda_to_mulled_targets(conda_targets)
        mulled_targets_str = "- " + "\n- ".join(map(conda_build_target_str, mulled_targets))

        if len(mulled_targets) < 1:
            ctx.log("Skipping registration, no targets discovered.")
            continue

        name = v2_image_name(mulled_targets)
        tag = "0"
        name_and_tag = "%s-%s" % (name, tag)
        target_filename = os.path.join(registry_target.output_directory, "%s.tsv" % name_and_tag)
        if os.path.exists(target_filename):
            ctx.log("Target file '%s' already exists, skipping" % target_filename)
            continue

        if targets_to_mulled_name(mulled_targets, hash_func='v2', namespace=kwds["mulled_namespace"]):
            ctx.vlog("quay repository already exists, skipping")
            continue

        if registry_target.has_pull_request_for(name):
            ctx.vlog("Found matching open pull request for [%s], skipping" % name)
            continue

        best_practice_requirements = True
        for conda_target in conda_targets:
            best_hit, exact = best_practice_search(conda_target, conda_context=conda_context, platform=BIOCONTAINERS_PLATFORM)
            if not best_hit:
                ctx.log("Target [%s] is not available in best practice channels - skipping" % conda_target)
                best_practice_requirements = False
            if not exact:
                ctx.log("Target version [%s] for package [%s] is not available in best practice channels - please specify the full version",
                        conda_target.version,
                        conda_target.package)

        if not best_practice_requirements:
            continue

        base_image = DEFAULT_BASE_IMAGE
        for conda_target in conda_targets:
            base_image = base_image_for_targets([conda_target], conda_context=conda_context)
            if base_image != DEFAULT_BASE_IMAGE:
                ctx.log("%s requires '%s' as base image" % (conda_target, base_image))
                break

        registry_target.write_targets(ctx, target_filename, mulled_targets, tag, base_image)
        tools_str = "\n".join(map(lambda p: "- " + os.path.basename(p), tool_paths))
        registry_target.handle_pull_request(ctx, name, target_filename, mulled_targets_str, tools_str, base_image, **kwds)
        combinations_added += 1


class RegistryTarget(object):
    """Abstraction around mulled container registry (both directory and Github repo)."""

    def __init__(self, ctx, **kwds):
        output_directory = kwds["output_directory"]
        pr_titles = []
        target_repository = None
        self.remote_name = DEFAULT_REMOTE_NAME
        do_pull_request = kwds.get("pull_request", True)
        if output_directory is None:
            target_repository = os.path.join(ctx.workspace, REGISTRY_TARGET_NAME)
            output_directory = os.path.join(target_repository, REGISTRY_TARGET_PATH)
            self.remote_name = clone_fork_branch(
                ctx,
                "https://github.com/%s" % REGISTRY_REPOSITORY,
                target_repository,
                fork=do_pull_request,
            ) or self.remote_name
            pr_titles = [pr.title for pr in open_prs(ctx)]

        self.do_pull_request = do_pull_request
        self.pr_titles = pr_titles
        self.output_directory = output_directory
        self.target_repository = target_repository

    def has_pull_request_for(self, name):
        has_pr = False
        if self.do_pull_request:
            if any([name in t for t in self.pr_titles]):
                has_pr = True

        return has_pr

    def handle_pull_request(self, ctx, name, target_filename, packages_str, tools_str, base_image, **kwds):
        if self.do_pull_request:
            message = kwds["message"]
            message = string.Template(message).safe_substitute({
                "hash": name,
                "packages": packages_str,
                "tools": tools_str,
                "base_image": base_image,
            })
            branch_name = name.replace(":", "-")
            branch(ctx, self.target_repository, branch_name, from_branch="master")
            add(ctx, self.target_repository, target_filename)
            commit(ctx, self.target_repository, message=message)
            force_push = kwds.get("force_push", False)
            push(ctx, repo_path=self.target_repository, to=self.remote_name, branch=branch_name, force=force_push)
            pull_request(ctx, self.target_repository, message=message, repo=REGISTRY_REPOSITORY)

    def write_targets(self, ctx, target_filename, mulled_targets, tag, base_image):
        with open(target_filename, "w") as f:
            targets = to_target_str(mulled_targets)
            f.write(string.Template(CONTENTS).safe_substitute(
                targets=targets,
                base_image=base_image,
                image_build=tag
                )
            )
            ctx.log("Wrote requirements [%s] to file [%s]" % (targets, target_filename))


def to_target_str(targets):
    target_strings = []
    for target in targets:
        if target.version:
            target_str = "%s=%s" % (target.package_name, target.version)
        else:
            target_str = target.package_name
        target_strings.append(target_str)
    return ",".join(target_strings)


def open_prs(ctx):
    repo = get_repository_object(ctx, REGISTRY_REPOSITORY)
    prs = [pr for pr in repo.get_pulls()]
    return prs