comparison env/lib/python3.7/site-packages/planemo/galaxy/profiles.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

4:79f47841a781

"""This modules describes the abstraction of a Galaxy profile.

This is a workspace with a specific default configuration and shed
tool setup. It is meant to be used with various serve commands.
"""
import json
import os
import shutil

from galaxy.tool_util.deps.commands import which

from planemo.config import (
    OptionSource,
)
from planemo.database import create_database_source
from .config import DATABASE_LOCATION_TEMPLATE

PROFILE_OPTIONS_JSON_NAME = "planemo_profile_options.json"
ALREADY_EXISTS_EXCEPTION = "Cannot create profile with name [%s], directory [%s] already exists."


def profile_exists(ctx, profile_name, **kwds):
    """Return a truthy value iff the specified profile already exists."""
    profile_directory = _profile_directory(ctx, profile_name)
    return os.path.exists(profile_directory)


def list_profiles(ctx, **kwds):
    """Return a list of current profile names."""
    return os.listdir(ctx.galaxy_profiles_directory)


def delete_profile(ctx, profile_name, **kwds):
    """Delete profile with the specified name."""
    profile_directory = _profile_directory(ctx, profile_name)
    profile_options = _read_profile_options(profile_directory)
    database_type = profile_options.get("database_type")
    if database_type != "sqlite":
        database_source = create_database_source(**kwds)
        database_identifier = _profile_to_database_identifier(profile_name)
        database_source.delete_database(
            database_identifier,
        )
    shutil.rmtree(profile_directory)


def create_profile(ctx, profile_name, **kwds):
    """Create a profile with the specified name."""
    engine_type = kwds.get("engine", "galaxy")
    profile_directory = _profile_directory(ctx, profile_name)
    if profile_exists(ctx, profile_name, **kwds):
        message = ALREADY_EXISTS_EXCEPTION % (
            profile_name, profile_directory
        )
        raise Exception(message)

    os.makedirs(profile_directory)
    create_for_engine = _create_profile_docker if engine_type == "docker_galaxy" else _create_profile_local
    stored_profile_options = create_for_engine(ctx, profile_directory, profile_name, kwds)

    profile_options_path = _stored_profile_options_path(profile_directory)
    with open(profile_options_path, "w") as f:
        json.dump(stored_profile_options, f)


def _create_profile_docker(ctx, profile_directory, profile_name, kwds):
    export_directory = os.path.join(profile_directory, "export")
    os.makedirs(export_directory)
    return {
        "engine": "docker_galaxy",
    }


def _create_profile_local(ctx, profile_directory, profile_name, kwds):
    database_type = kwds.get("database_type", "auto")
    if database_type == "auto":
        if which("psql"):
            database_type = "postgres"
        elif which("docker"):
            database_type = "postgres_docker"
        else:
            database_type = "sqlite"

    if database_type != "sqlite":
        database_source = create_database_source(**kwds)
        database_identifier = _profile_to_database_identifier(profile_name)
        database_source.create_database(
            database_identifier,
        )
        database_connection = database_source.sqlalchemy_url(database_identifier)
    else:
        database_location = os.path.join(profile_directory, "galaxy.sqlite")
        database_connection = DATABASE_LOCATION_TEMPLATE % database_location

    return {
        "database_type": database_type,
        "database_connection": database_connection,
        "engine": "galaxy",
    }


def ensure_profile(ctx, profile_name, **kwds):
    """Ensure a Galaxy profile exists and return profile defaults."""
    if not profile_exists(ctx, profile_name, **kwds):
        create_profile(ctx, profile_name, **kwds)

    return _profile_options(ctx, profile_name, **kwds)


def _profile_options(ctx, profile_name, **kwds):
    profile_directory = _profile_directory(ctx, profile_name)
    profile_options = _read_profile_options(profile_directory)
    specified_engine_type = kwds.get("engine", "galaxy")
    profile_engine_type = profile_options["engine"]
    if specified_engine_type != profile_engine_type:
        if ctx.get_option_source("engine") == OptionSource.cli:
            raise Exception("Configured profile engine type [%s] does not match specified engine type [%s].")

    if profile_engine_type == "docker_galaxy":
        engine_options = dict(
            export_directory=os.path.join(profile_directory, "export")
        )
    else:
        file_path = os.path.join(profile_directory, "files")
        shed_tool_path = os.path.join(profile_directory, "shed_tools")
        shed_tool_conf = os.path.join(profile_directory, "shed_tool_conf.xml")
        tool_dependency_dir = os.path.join(profile_directory, "deps")

        engine_options = dict(
            file_path=file_path,
            tool_dependency_dir=tool_dependency_dir,
            shed_tool_conf=shed_tool_conf,
            shed_tool_path=shed_tool_path,
            galaxy_brand=profile_name,
        )
    profile_options.update(engine_options)
    profile_options["galaxy_brand"] = profile_name
    return profile_options


def _profile_to_database_identifier(profile_name):
    char_lst = [c if c.isalnum() else "_" for c in profile_name]
    return "plnmoprof_%s" % "".join(char_lst)


def _read_profile_options(profile_directory):
    profile_options_path = _stored_profile_options_path(profile_directory)
    with open(profile_options_path, "r") as f:
        profile_options = json.load(f)
    return profile_options


def _stored_profile_options_path(profile_directory):
    profile_options_path = os.path.join(
        profile_directory, PROFILE_OPTIONS_JSON_NAME
    )
    return profile_options_path


def _profile_directory(ctx, profile_name):
    return os.path.join(ctx.galaxy_profiles_directory, profile_name)


__all__ = (
    "create_profile",
    "delete_profile",
    "ensure_profile",
    "list_profiles",
)