Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/planemo/galaxy/profiles.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/planemo/galaxy/profiles.py Sat May 02 07:14:21 2020 -0400 @@ -0,0 +1,169 @@ +"""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", +)