Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tool_util.deps.conda_util

import functools
import hashlib
import json
import logging
import os
import re
import shlex
import shutil
import sys
import tempfile

import packaging.version

from galaxy.util import (
    commands,
    smart_str,
    unicodify
)
from . import installable

log = logging.getLogger(__name__)

# Not sure there are security concerns, lets just fail fast if we are going
# break shell commands we are building.
SHELL_UNSAFE_PATTERN = re.compile(r"[\s\"']")

IS_OS_X = sys.platform == "darwin"

VERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@(.*)")
UNVERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@_uv_")
USE_PATH_EXEC_DEFAULT = False
CONDA_PACKAGE_SPECS = ("conda=4.6.14", "'pyopenssl>=22.1.0'")
CONDA_BUILD_VERSION = "3.17.8"
USE_LOCAL_DEFAULT = False


def conda_link():
    if IS_OS_X:
        url = "https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-MacOSX-x86_64.sh"
    else:
        if sys.maxsize > 2**32:
            url = "https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh"
        else:
            url = "https://repo.anaconda.com/miniconda/Miniconda3-4.5.12-Linux-x86.sh"
    return url


def find_conda_prefix(conda_prefix=None):
    """ If supplied conda_prefix is not set, default to the default location
    for Miniconda installs.
    """
    if conda_prefix is None:
        home = os.path.expanduser("~")
        miniconda_2_dest = os.path.join(home, "miniconda2")
        miniconda_3_dest = os.path.join(home, "miniconda3")
        anaconda_2_dest = os.path.join(home, "anaconda2")
        anaconda_3_dest = os.path.join(home, "anaconda3")
        # Prefer miniconda3 install if both available
        if os.path.exists(miniconda_3_dest):
            return miniconda_3_dest
        elif os.path.exists(miniconda_2_dest):
            return miniconda_2_dest
        elif os.path.exists(anaconda_3_dest):
            return anaconda_3_dest
        elif os.path.exists(anaconda_2_dest):
            return anaconda_2_dest
        else:
            return miniconda_3_dest
    return conda_prefix


[docs]class CondaContext(installable.InstallableContext): installable_description = "Conda"
[docs] def __init__(self, conda_prefix=None, conda_exec=None, shell_exec=None, debug=False, ensure_channels='', condarc_override=None, use_path_exec=USE_PATH_EXEC_DEFAULT, copy_dependencies=False, use_local=USE_LOCAL_DEFAULT): self.condarc_override = condarc_override if not conda_exec and use_path_exec: conda_exec = commands.which("conda") if conda_exec: conda_exec = os.path.normpath(conda_exec) self.conda_exec = conda_exec self.debug = debug self.shell_exec = shell_exec or commands.shell self.copy_dependencies = copy_dependencies if conda_prefix is None: info = self.conda_info() if info and "default_prefix" in info: conda_prefix = info["default_prefix"] if conda_prefix is None: conda_prefix = find_conda_prefix(conda_prefix) self.conda_prefix = conda_prefix if conda_exec is None: self.conda_exec = self._bin("conda") if ensure_channels: if not isinstance(ensure_channels, list): ensure_channels = [c for c in ensure_channels.split(",") if c] else: ensure_channels = None self.ensure_channels = ensure_channels self.use_local = use_local self._reset_conda_properties()
def _reset_conda_properties(self): self._conda_version = None self._conda_build_available = None @property def conda_version(self): if self._conda_version is None: self._guess_conda_properties() return self._conda_version @property def conda_build_available(self): if self._conda_build_available is None: self._guess_conda_properties() return self._conda_build_available def _guess_conda_properties(self): info = self.conda_info() self._conda_version = packaging.version.parse(info["conda_version"]) self._conda_build_available = False conda_build_version = info.get("conda_build_version") if conda_build_version and conda_build_version != "not installed": try: packaging.version.parse(conda_build_version) self._conda_build_available = True except Exception: pass @property def _override_channels_args(self): override_channels_args = [] if self.ensure_channels: override_channels_args.append("--override-channels") for channel in self.ensure_channels: override_channels_args.extend(["--channel", channel]) return override_channels_args
[docs] def ensure_conda_build_installed_if_needed(self): if self.use_local and not self.conda_build_available: conda_targets = [CondaTarget("conda-build", version=CONDA_BUILD_VERSION)] # Cannot use --use-local during installation of conda-build. return install_conda_targets(conda_targets, conda_context=self, env_name=None, allow_local=False) else: return 0
[docs] def conda_info(self): if self.conda_exec is not None: info_out = commands.execute([self.conda_exec, "info", "--json"]) info_out = unicodify(info_out) info = json.loads(info_out) return info else: return None
[docs] def is_conda_installed(self): """ Check if conda_exec exists """ if os.path.exists(self.conda_exec): return True else: return False
[docs] def can_install_conda(self): """ If conda_exec is set to a path outside of conda_prefix, there is no use installing conda into conda_prefix, since it can't be used by galaxy. If conda_exec equals conda_prefix/bin/conda, we can install conda if either conda_prefix does not exist or is empty. """ conda_exec = os.path.abspath(self.conda_exec) conda_prefix_plus_exec = os.path.abspath(os.path.join(self.conda_prefix, 'bin/conda')) if conda_exec == conda_prefix_plus_exec: if not os.path.exists(self.conda_prefix): return True elif os.listdir(self.conda_prefix) == []: os.rmdir(self.conda_prefix) # Conda's install script fails if path exists (even if empty). return True else: log.warning("Cannot install Conda because conda_prefix '%s' exists and is not empty.", self.conda_prefix) return False else: log.warning("Skipping installation of Conda into conda_prefix '%s', " "since conda_exec '%s' is set to a path outside of conda_prefix.", self.conda_prefix, self.conda_exec) return False
[docs] def exec_command(self, operation, args, stdout_path=None): """ Execute the requested command. Return the process exit code (i.e. 0 in case of success). """ cmd = [self.conda_exec] cmd.extend(operation.split()) if self.debug: cmd.append("--debug") cmd.extend(args) env = {} if self.condarc_override: env["CONDARC"] = self.condarc_override cmd_string = ' '.join(map(shlex.quote, cmd)) kwds = dict() try: if stdout_path: kwds['stdout'] = open(stdout_path, 'w') cmd_string += f" > '{stdout_path}'" conda_exec_home = env['HOME'] = tempfile.mkdtemp(prefix='conda_exec_home_') # We don't want to pollute ~/.conda, which may not even be writable log.debug("Executing command: %s", cmd_string) return self.shell_exec(cmd, env=env, **kwds) except Exception: log.exception("Failed to execute command: %s", cmd_string) return 1 finally: if kwds.get('stdout'): kwds['stdout'].close() if conda_exec_home: shutil.rmtree(conda_exec_home, ignore_errors=True)
[docs] def exec_create(self, args, allow_local=True, stdout_path=None): """ Return the process exit code (i.e. 0 in case of success). """ for try_strict in [True, False]: create_args = ["-y", "--quiet"] if try_strict: if self.conda_version >= packaging.version.parse("4.7.5"): create_args.append("--strict-channel-priority") else: continue if allow_local and self.use_local: create_args.append("--use-local") create_args.extend(self._override_channels_args) create_args.extend(args) ret = self.exec_command("create", create_args, stdout_path=stdout_path) if ret == 0: break return ret
[docs] def exec_remove(self, args): """ Remove a conda environment using conda env remove -y --name `args`. Return the process exit code (i.e. 0 in case of success). """ remove_args = [ "-y", "--name" ] remove_args.extend(args) return self.exec_command("env remove", remove_args)
[docs] def exec_install(self, args, allow_local=True, stdout_path=None): """ Return the process exit code (i.e. 0 in case of success). """ for try_strict in [True, False]: install_args = ["-y"] if try_strict: if self.conda_version >= packaging.version.parse("4.7.5"): install_args.append("--strict-channel-priority") else: continue if allow_local and self.use_local: install_args.append("--use-local") install_args.extend(self._override_channels_args) install_args.extend(args) ret = self.exec_command("install", install_args, stdout_path=stdout_path) if ret == 0: break if ret == 0: self._reset_conda_properties() return ret
[docs] def exec_clean(self, args=None, quiet=False): """ Clean up after conda installation. Return the process exit code (i.e. 0 in case of success). """ clean_args = [ "--tarballs", "-y" ] if args: clean_args.extend(args) stdout_path = None if quiet: stdout_path = "/dev/null" return self.exec_command("clean", clean_args, stdout_path=stdout_path)
[docs] def export_list(self, name, path): """ Return the process exit code (i.e. 0 in case of success). """ return self.exec_command("list", [ "--name", name, "--export" ], stdout_path=path)
[docs] def env_path(self, env_name): return os.path.join(self.envs_path, env_name)
@property def envs_path(self): return os.path.join(self.conda_prefix, "envs")
[docs] def has_env(self, env_name): env_path = self.env_path(env_name) return os.path.isdir(env_path)
@property def deactivate(self): return self._bin("deactivate") @property def activate(self): return self._bin("activate")
[docs] def is_installed(self): return self.is_conda_installed()
[docs] def can_install(self): return self.can_install_conda()
@property def parent_path(self): return os.path.dirname(os.path.abspath(self.conda_prefix)) def _bin(self, name): return os.path.join(self.conda_prefix, "bin", name)
def installed_conda_targets(conda_context): envs_path = conda_context.envs_path dir_contents = os.listdir(envs_path) if os.path.exists(envs_path) else [] for name in dir_contents: versioned_match = VERSIONED_ENV_DIR_NAME.match(name) if versioned_match: yield CondaTarget(versioned_match.group(1), versioned_match.group(2)) unversioned_match = UNVERSIONED_ENV_DIR_NAME.match(name) if unversioned_match: yield CondaTarget(unversioned_match.group(1))
[docs]class CondaTarget:
[docs] def __init__(self, package, version=None, channel=None): if SHELL_UNSAFE_PATTERN.search(package) is not None: raise ValueError(f"Invalid package [{package}] encountered.") self.package = package if version and SHELL_UNSAFE_PATTERN.search(version) is not None: raise ValueError(f"Invalid version [{version}] encountered.") self.version = version if channel and SHELL_UNSAFE_PATTERN.search(channel) is not None: raise ValueError(f"Invalid version [{channel}] encountered.") self.channel = channel
def __str__(self): attributes = f"package={self.package}" if self.version is not None: attributes = f"{self.package},version={self.version}" else: attributes = f"{self.package},unversioned" if self.channel: attributes = "%s,channel=%s" % self.channel return f"CondaTarget[{attributes}]" __repr__ = __str__ @property def package_specifier(self): """ Return a package specifier as consumed by conda install/create. """ if self.version: return f"{self.package}={self.version}" else: return self.package @property def install_environment(self): """ The dependency resolution and installation frameworks will expect each target to be installed it its own environment with a fixed and predictable name given package and version. """ if self.version: return f"__{self.package}@{self.version}" else: return f"__{self.package}@_uv_" def __hash__(self): return hash((self.package, self.version, self.channel)) def __eq__(self, other): if isinstance(other, self.__class__): return (self.package, self.version, self.channel) == (other.package, other.version, other.channel) return False def __ne__(self, other): return not(self == other)
def hash_conda_packages(conda_packages, conda_target=None): """ Produce a unique hash on supplied packages. TODO: Ideally we would do this in such a way that preserved environments. """ h = hashlib.new('sha256') for conda_package in conda_packages: h.update(smart_str(conda_package.install_environment)) return h.hexdigest() # shell makes sense for planemo, in Galaxy this should just execute # these commands as Python
[docs]def install_conda(conda_context, force_conda_build=False): with tempfile.NamedTemporaryFile(suffix=".sh", prefix="conda_install", delete=False) as temp: script_path = temp.name download_cmd = commands.download_command(conda_link(), to=script_path) install_cmd = ['bash', script_path, '-b', '-p', conda_context.conda_prefix] package_targets = list(CONDA_PACKAGE_SPECS) if force_conda_build or conda_context.use_local: package_targets.append(f"conda-build={CONDA_BUILD_VERSION}") log.info("Installing conda, this may take several minutes.") try: exit_code = conda_context.shell_exec(download_cmd) if exit_code: return exit_code exit_code = conda_context.shell_exec(install_cmd) except Exception: log.exception('Failed to install conda') return 1 finally: if os.path.exists(script_path): os.remove(script_path) if exit_code: return exit_code return conda_context.exec_install(package_targets, allow_local=False)
def install_conda_targets(conda_targets, conda_context, env_name=None, allow_local=True): """ Return the process exit code (i.e. 0 in case of success). """ if env_name is not None: create_args = [ "--name", env_name, # environment for package ] for conda_target in conda_targets: create_args.append(conda_target.package_specifier) return conda_context.exec_create(create_args, allow_local=allow_local) else: return conda_context.exec_install([t.package_specifier for t in conda_targets], allow_local=allow_local)
[docs]def install_conda_target(conda_target, conda_context, skip_environment=False): """ Install specified target into a its own environment. Return the process exit code (i.e. 0 in case of success). """ if not skip_environment: create_args = [ "--name", conda_target.install_environment, # environment for package conda_target.package_specifier, ] return conda_context.exec_create(create_args) else: return conda_context.exec_install([conda_target.package_specifier])
def cleanup_failed_install_of_environment(env, conda_context): if conda_context.has_env(env): conda_context.exec_remove([env]) def cleanup_failed_install(conda_target, conda_context=None): cleanup_failed_install_of_environment(conda_target.install_environment, conda_context=conda_context) def best_search_result(conda_target, conda_context, channels_override=None, offline=False, platform=None): """Find best "conda search" result for specified target. Return ``None`` if no results match. """ search_cmd = [] conda_exec = conda_context.conda_exec if isinstance(conda_exec, list): # for CondaInDockerContext search_cmd.extend(conda_exec) else: search_cmd.append(conda_exec) search_cmd.extend(["search", "--full-name", "--json"]) if offline: search_cmd.append("--offline") if platform: search_cmd.extend(['--platform', platform]) if channels_override: search_cmd.append("--override-channels") for channel in channels_override: search_cmd.extend(["--channel", channel]) else: search_cmd.extend(conda_context._override_channels_args) search_cmd.append(conda_target.package) try: res = commands.execute(search_cmd) res = unicodify(res) # Use python's stable list sorting to sort by date, # then build_number, then version. The top of the list # then is the newest version with the newest build and # the latest update time. hits = json.loads(res).get(conda_target.package, [])[::-1] hits = sorted(hits, key=lambda hit: hit['build_number'], reverse=True) hits = sorted(hits, key=lambda hit: packaging.version.parse(hit['version']), reverse=True) except commands.CommandLineException: log.error("Could not execute: '%s'", search_cmd) hits = [] if len(hits) == 0: return (None, None) best_result = (hits[0], False) for hit in hits: if is_search_hit_exact(conda_target, hit): best_result = (hit, True) break return best_result def is_search_hit_exact(conda_target, search_hit): target_version = conda_target.version # It'd be nice to make request verson of 1.0 match available # version of 1.0.3 or something like that. return not target_version or search_hit['version'] == target_version def is_conda_target_installed(conda_target, conda_context): # fail by default if conda_context.has_env(conda_target.install_environment): return True else: return False def filter_installed_targets(conda_targets, conda_context): installed = functools.partial(is_conda_target_installed, conda_context=conda_context) return list(filter(installed, conda_targets)) def build_isolated_environment( conda_packages, conda_context, path=None, copy=False, quiet=False, ): """ Build a new environment (or reuse an existing one from hashes) for specified conda packages. """ if not isinstance(conda_packages, list): conda_packages = [conda_packages] # Lots we could do in here, hashing, checking revisions, etc... tempdir = None try: hash = hash_conda_packages(conda_packages) tempdir = tempfile.mkdtemp(prefix="jobdeps", suffix=hash) tempdir_name = os.path.basename(tempdir) export_paths = [] for conda_package in conda_packages: name = conda_package.install_environment export_path = os.path.join(tempdir, name) conda_context.export_list( name, export_path ) export_paths.append(export_path) create_args = ["--unknown"] # Works in 3.19, 4.0 - 4.2 - not in 4.3. # Adjust fix if they fix Conda - xref # - https://github.com/galaxyproject/galaxy/issues/3635 # - https://github.com/conda/conda/issues/2035 offline_works = (conda_context.conda_version < packaging.version.parse("4.3")) or \ (conda_context.conda_version >= packaging.version.parse("4.4")) if offline_works: create_args.extend(["--offline"]) else: create_args.extend(["--use-index-cache"]) if path is None: create_args.extend(["--name", tempdir_name]) else: create_args.extend(["--prefix", path]) if copy: create_args.append("--copy") for export_path in export_paths: create_args.extend([ "--file", export_path ]) stdout_path = None if quiet: stdout_path = "/dev/null" if path is not None and os.path.exists(path): exit_code = conda_context.exec_install(create_args, stdout_path=stdout_path) else: exit_code = conda_context.exec_create(create_args, stdout_path=stdout_path) return (path or tempdir_name, exit_code) finally: conda_context.exec_clean(quiet=quiet) if tempdir is not None: shutil.rmtree(tempdir) def requirement_to_conda_targets(requirement): conda_target = None if requirement.type == "package": conda_target = CondaTarget(requirement.name, version=requirement.version) return conda_target
[docs]def requirements_to_conda_targets(requirements): conda_targets = (requirement_to_conda_targets(_) for _ in requirements) return [c for c in conda_targets if c is not None]
__all__ = ( 'CondaContext', 'CondaTarget', 'install_conda', 'install_conda_target', 'requirements_to_conda_targets', )