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.tools.deps.resolvers.conda
"""
This is still an experimental module and there will almost certainly be backward
incompatible changes coming.
"""
import logging
import os
import re
import galaxy.tools.deps.installable
import galaxy.tools.deps.requirements
from ..conda_util import (
build_isolated_environment,
cleanup_failed_install,
cleanup_failed_install_of_environment,
CondaContext,
CondaTarget,
hash_conda_packages,
install_conda,
install_conda_target,
install_conda_targets,
installed_conda_targets,
is_conda_target_installed,
USE_PATH_EXEC_DEFAULT,
)
from ..resolvers import (
Dependency,
DependencyException,
DependencyResolver,
InstallableDependencyResolver,
ListableDependencyResolver,
MappableDependencyResolver,
MultipleDependencyResolver,
NullDependency,
SpecificationPatternDependencyResolver,
)
DEFAULT_BASE_PATH_DIRECTORY = "_conda"
DEFAULT_CONDARC_OVERRIDE = "_condarc"
# Conda channel order from highest to lowest, following the one used in
# https://github.com/bioconda/bioconda-recipes/blob/master/config.yml , but
# adding `iuc` as first channel (for Galaxy-specific packages) and `r` as last
# (for old R packages)
DEFAULT_ENSURE_CHANNELS = "iuc,bioconda,conda-forge,defaults"
CONDA_SOURCE_CMD = """[ "$CONDA_DEFAULT_ENV" = "%s" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. %s '%s' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done """
log = logging.getLogger(__name__)
[docs]class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, ListableDependencyResolver, InstallableDependencyResolver, SpecificationPatternDependencyResolver, MappableDependencyResolver):
dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['conda_prefix', 'versionless', 'ensure_channels', 'auto_install']
resolver_type = "conda"
config_options = {
'prefix': None,
'exec': None,
'debug': None,
'ensure_channels': DEFAULT_ENSURE_CHANNELS,
'auto_install': False,
'auto_init': True,
'copy_dependencies': False,
'use_local': False,
}
_specification_pattern = re.compile(r"https\:\/\/anaconda.org\/\w+\/\w+")
[docs] def __init__(self, dependency_manager, **kwds):
self.can_uninstall_dependencies = True
self._setup_mapping(dependency_manager, **kwds)
self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
self.dependency_manager = dependency_manager
def get_option(name):
return dependency_manager.get_resolver_option(self, name, explicit_resolver_options=kwds)
# Conda context options (these define the environment)
conda_prefix = get_option("prefix")
if conda_prefix is None:
conda_prefix = os.path.join(
dependency_manager.default_base_path, DEFAULT_BASE_PATH_DIRECTORY
)
conda_prefix = os.path.abspath(conda_prefix)
self.conda_prefix_parent = os.path.dirname(conda_prefix)
condarc_override = get_option("condarc_override")
if condarc_override is None:
condarc_override = os.path.join(
dependency_manager.default_base_path, DEFAULT_CONDARC_OVERRIDE
)
copy_dependencies = _string_as_bool(get_option("copy_dependencies"))
use_local = _string_as_bool(get_option("use_local"))
conda_exec = get_option("exec")
debug = _string_as_bool(get_option("debug"))
ensure_channels = get_option("ensure_channels")
use_path_exec = get_option("use_path_exec")
if use_path_exec is None:
use_path_exec = USE_PATH_EXEC_DEFAULT
else:
use_path_exec = _string_as_bool(use_path_exec)
if ensure_channels is None:
ensure_channels = DEFAULT_ENSURE_CHANNELS
conda_context = CondaContext(
conda_prefix=conda_prefix,
conda_exec=conda_exec,
debug=debug,
ensure_channels=ensure_channels,
condarc_override=condarc_override,
use_path_exec=use_path_exec,
copy_dependencies=copy_dependencies,
use_local=use_local,
)
self.ensure_channels = ensure_channels
# Conda operations options (these define how resolution will occur)
auto_install = _string_as_bool(get_option("auto_install"))
self.auto_init = _string_as_bool(get_option("auto_init"))
self.conda_context = conda_context
self.disabled = not galaxy.tools.deps.installable.ensure_installed(conda_context, install_conda, self.auto_init)
if self.auto_init and not self.disabled:
self.conda_context.ensure_conda_build_installed_if_needed()
self.auto_install = auto_install
self.copy_dependencies = copy_dependencies
[docs] def uninstall(self, requirements):
"""Uninstall requirements installed by install_all or multiple install statements."""
all_resolved = [r for r in self.resolve_all(requirements) if r.dependency_type]
if not all_resolved:
all_resolved = [self.resolve(requirement) for requirement in requirements]
all_resolved = [r for r in all_resolved if r.dependency_type]
if not all_resolved:
return None
environments = set([os.path.basename(dependency.environment_path) for dependency in all_resolved])
return self.uninstall_environments(environments)
[docs] def uninstall_environments(self, environments):
environments = [env if not env.startswith(self.conda_context.envs_path) else os.path.basename(env) for env in environments]
return_codes = [self.conda_context.exec_remove([env]) for env in environments]
final_return_code = 0
for env, return_code in zip(environments, return_codes):
if return_code == 0:
log.debug("Conda environment '%s' successfully removed." % env)
else:
log.debug("Conda environment '%s' could not be removed." % env)
final_return_code = return_code
return final_return_code
[docs] def install_all(self, conda_targets):
env = self.merged_environment_name(conda_targets)
return_code = install_conda_targets(conda_targets, conda_context=self.conda_context, env_name=env)
if return_code != 0:
is_installed = False
else:
# Recheck if installed
is_installed = self.conda_context.has_env(env)
if not is_installed:
log.debug("Removing failed conda install of {}".format(str(conda_targets)))
cleanup_failed_install_of_environment(env, conda_context=self.conda_context)
return is_installed
[docs] def resolve_all(self, requirements, **kwds):
"""
Some combinations of tool requirements need to be resolved all at once, so that Conda can select a compatible
combination of dependencies. This method returns a list of MergedCondaDependency instances (one for each requirement)
if all requirements have been successfully resolved, or an empty list if any of the requirements could not be resolved.
Parameters specific to this resolver are:
preserve_python_environment: Boolean, controls whether the python environment should be maintained during job creation for tools
that rely on galaxy being importable.
install: Controls if `requirements` should be installed. If `install` is True and the requirements are not installed
an attempt is made to install the requirements. If `install` is None requirements will only be installed if
`conda_auto_install` has been activated and the requirements are not yet installed. If `install` is
False will not install requirements.
"""
if len(requirements) == 0:
return []
if not os.path.isdir(self.conda_context.conda_prefix):
return []
for requirement in requirements:
if requirement.type != "package":
return []
ToolRequirements = galaxy.tools.deps.requirements.ToolRequirements
expanded_requirements = ToolRequirements([self._expand_requirement(r) for r in requirements])
if self.versionless:
conda_targets = [CondaTarget(r.name, version=None) for r in expanded_requirements]
else:
conda_targets = [CondaTarget(r.name, version=r.version) for r in expanded_requirements]
preserve_python_environment = kwds.get("preserve_python_environment", False)
env = self.merged_environment_name(conda_targets)
dependencies = []
is_installed = self.conda_context.has_env(env)
install = kwds.get('install', None)
if install is None:
# Default behavior, install dependencies if conda_auto_install is active.
install = not is_installed and self.auto_install
elif install:
# Install has been set to True, install if not yet installed.
install = not is_installed
if install:
is_installed = self.install_all(conda_targets)
if is_installed:
for requirement in requirements:
dependency = MergedCondaDependency(
self.conda_context,
self.conda_context.env_path(env),
exact=not self.versionless or requirement.version is None,
name=requirement.name,
version=requirement.version,
preserve_python_environment=preserve_python_environment,
)
dependencies.append(dependency)
return dependencies
[docs] def merged_environment_name(self, conda_targets):
if len(conda_targets) > 1:
# For continuity with mulled containers this is kind of nice.
return "mulled-v1-%s" % hash_conda_packages(conda_targets)
else:
assert len(conda_targets) == 1
return conda_targets[0].install_environment
[docs] def resolve(self, requirement, **kwds):
requirement = self._expand_requirement(requirement)
name, version, type = requirement.name, requirement.version, requirement.type
# Check for conda just not being there, this way we can enable
# conda by default and just do nothing in not configured.
if not os.path.isdir(self.conda_context.conda_prefix):
return NullDependency(version=version, name=name)
if type != "package":
return NullDependency(version=version, name=name)
exact = not self.versionless or version is None
if self.versionless:
version = None
conda_target = CondaTarget(name, version=version)
is_installed = is_conda_target_installed(
conda_target, conda_context=self.conda_context
)
preserve_python_environment = kwds.get("preserve_python_environment", False)
job_directory = kwds.get("job_directory", None)
install = kwds.get('install', None)
if install is None:
install = not is_installed and self.auto_install
elif install:
install = not is_installed
if install:
is_installed = self.install_dependency(name=name, version=version, type=type)
if not is_installed:
return NullDependency(version=version, name=name)
# Have installed conda_target and job_directory to send it to.
# If dependency is for metadata generation, store environment in conda-metadata-env
if kwds.get("metadata", False):
conda_env = "conda-metadata-env"
else:
conda_env = "conda-env"
if job_directory:
conda_environment = os.path.join(job_directory, conda_env)
else:
conda_environment = self.conda_context.env_path(conda_target.install_environment)
return CondaDependency(
self.conda_context,
conda_environment,
exact,
name,
version,
preserve_python_environment=preserve_python_environment,
)
def _expand_requirement(self, requirement):
return self._expand_specs(self._expand_mappings(requirement))
[docs] def unused_dependency_paths(self, toolbox_requirements_status):
"""
Identify all local environments that are not needed to build requirements_status.
We try to resolve the requirements, and we note every environment_path that has been taken.
"""
used_paths = set()
for dependencies in toolbox_requirements_status.values():
for dependency in dependencies:
if dependency.get('dependency_type') == 'conda':
path = os.path.basename(dependency['environment_path'])
used_paths.add(path)
dir_contents = set(os.listdir(self.conda_context.envs_path) if os.path.exists(self.conda_context.envs_path) else [])
unused_paths = dir_contents.difference(used_paths) # New set with paths in dir_contents but not in used_paths
unused_paths = [os.path.join(self.conda_context.envs_path, p) for p in unused_paths]
return unused_paths
[docs] def list_dependencies(self):
for install_target in installed_conda_targets(self.conda_context):
name = install_target.package
version = install_target.version
yield self._to_requirement(name, version)
[docs] def install_dependency(self, name, version, type, **kwds):
"Returns True on (seemingly) successfull installation"
if type != "package":
log.warning("Cannot install dependencies of type '%s'" % type)
return False
if self.versionless:
version = None
conda_target = CondaTarget(name, version=version)
is_installed = is_conda_target_installed(
conda_target, conda_context=self.conda_context
)
if is_installed:
return is_installed
return_code = install_conda_target(conda_target, conda_context=self.conda_context)
if return_code != 0:
is_installed = False
else:
# Recheck if installed
is_installed = is_conda_target_installed(
conda_target, conda_context=self.conda_context
)
if not is_installed:
log.debug("Removing failed conda install of {}, version '{}'".format(name, version))
cleanup_failed_install(conda_target, conda_context=self.conda_context)
return is_installed
@property
def prefix(self):
return self.conda_context.conda_prefix
class MergedCondaDependency(Dependency):
dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['environment_path', 'name', 'version']
dependency_type = 'conda'
def __init__(self, conda_context, environment_path, exact, name=None, version=None, preserve_python_environment=False):
self.activate = conda_context.activate
self.conda_context = conda_context
self.environment_path = environment_path
self._exact = exact
self._name = name
self._version = version
self.cache_path = None
self._preserve_python_environment = preserve_python_environment
@property
def exact(self):
return self._exact
@property
def name(self):
return self._name
@property
def version(self):
return self._version
def shell_commands(self):
if self._preserve_python_environment:
# On explicit testing the only such requirement I am aware of is samtools - and it seems to work
# fine with just appending the PATH as done below. Other tools may require additional
# variables in the future.
return """export PATH=$PATH:'%s/bin' """ % (
self.environment_path,
)
else:
return CONDA_SOURCE_CMD % (
self.environment_path,
self.activate,
self.environment_path
)
class CondaDependency(Dependency):
dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['environment_path', 'name', 'version']
dependency_type = 'conda'
cacheable = True
def __init__(self, conda_context, environment_path, exact, name=None, version=None, preserve_python_environment=False):
self.activate = conda_context.activate
self.conda_context = conda_context
self.environment_path = environment_path
self._exact = exact
self._name = name
self._version = version
self.cache_path = None
self._preserve_python_environment = preserve_python_environment
@property
def exact(self):
return self._exact
@property
def name(self):
return self._name
@property
def version(self):
return self._version
def build_cache(self, cache_path):
self.set_cache_path(cache_path)
self.build_environment()
def set_cache_path(self, cache_path):
self.cache_path = cache_path
self.environment_path = cache_path
def build_environment(self):
env_path, exit_code = build_isolated_environment(
CondaTarget(self.name, self.version),
conda_context=self.conda_context,
path=self.environment_path,
copy=self.conda_context.copy_dependencies,
)
if exit_code:
if len(os.path.abspath(self.environment_path)) > 79:
# TODO: remove this once conda_build version 2 is released and packages have been rebuilt.
raise DependencyException("Conda dependency failed to build job environment. "
"This is most likely a limitation in conda. "
"You can try to shorten the path to the job_working_directory.")
raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")
def shell_commands(self):
if not self.cache_path:
# Build an isolated environment if not using a cached dependency manager
self.build_environment()
if self._preserve_python_environment:
# On explicit testing the only such requirement I am aware of is samtools - and it seems to work
# fine with just appending the PATH as done below. Other tools may require additional
# variables in the future.
return """export PATH=$PATH:'%s/bin' """ % (
self.environment_path,
)
else:
return CONDA_SOURCE_CMD % (
self.environment_path,
self.activate,
self.environment_path
)
def _string_as_bool(value):
return str(value).lower() == "true"
__all__ = ('CondaDependencyResolver', 'DEFAULT_ENSURE_CHANNELS')