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Source code for galaxy.model.tool_shed_install
import logging
import os
from enum import Enum
from typing import TYPE_CHECKING
from galaxy.util import asbool
from galaxy.util.bunch import Bunch
from galaxy.util.dictifiable import Dictifiable
from galaxy.util.tool_shed import common_util
log = logging.getLogger(__name__)
if TYPE_CHECKING:
from sqlalchemy.schema import Table
class _HasTable:
table: Table
else:
_HasTable = object
[docs]class ToolShedRepository(_HasTable):
dict_collection_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']
dict_element_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']
[docs] class installation_status(str, Enum):
NEW = 'New'
CLONING = 'Cloning'
SETTING_TOOL_VERSIONS = 'Setting tool versions'
INSTALLING_REPOSITORY_DEPENDENCIES = 'Installing repository dependencies'
INSTALLING_TOOL_DEPENDENCIES = 'Installing tool dependencies'
LOADING_PROPRIETARY_DATATYPES = 'Loading proprietary datatypes'
INSTALLED = 'Installed'
DEACTIVATED = 'Deactivated'
ERROR = 'Error'
UNINSTALLED = 'Uninstalled'
[docs] class states(str, Enum):
INSTALLING = 'running'
OK = 'ok'
WARNING = 'queued'
ERROR = 'error'
UNINSTALLED = 'deleted_new'
def __init__(self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None,
changeset_revision=None, ctx_rev=None, metadata=None, includes_datatypes=False, tool_shed_status=None, deleted=False,
uninstalled=False, dist_to_shed=False, status=None, error_message=None):
self.id = id
self.create_time = create_time
self.tool_shed = tool_shed
self.name = name
self.description = description
self.owner = owner
self.installed_changeset_revision = installed_changeset_revision
self.changeset_revision = changeset_revision
self.ctx_rev = ctx_rev
self.metadata = metadata or {}
self.includes_datatypes = includes_datatypes
self.tool_shed_status = tool_shed_status
self.deleted = deleted
self.uninstalled = uninstalled
self.dist_to_shed = dist_to_shed
self.status = status
self.error_message = error_message
[docs] def as_dict(self, value_mapper=None):
return self.to_dict(view='element', value_mapper=value_mapper)
@property
def can_install(self):
return self.status == self.installation_status.NEW
@property
def can_reset_metadata(self):
return self.status == self.installation_status.INSTALLED
@property
def can_uninstall(self):
return self.status != self.installation_status.UNINSTALLED
@property
def can_deactivate(self):
return self.status not in [self.installation_status.DEACTIVATED,
self.installation_status.ERROR,
self.installation_status.UNINSTALLED]
@property
def can_reinstall_or_activate(self):
return self.deleted
[docs] def get_sharable_url(self, app):
return common_util.get_tool_shed_repository_url(app, self.tool_shed, self.owner, self.name)
@property
def shed_config_filename(self):
return self.metadata.get('shed_config_filename')
@shed_config_filename.setter
def shed_config_filename(self, value):
self.metadata['shed_config_filename'] = os.path.abspath(value)
[docs] def get_shed_config_dict(self, app):
"""
Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry
in the shed_tool_conf_dict.
"""
if self.shed_config_filename:
shed_config_dict = app.toolbox.get_shed_config_dict_by_filename(self.shed_config_filename)
if shed_config_dict:
return shed_config_dict
return self.guess_shed_config(app)
[docs] def get_tool_relative_path(self, app):
# This is a somewhat public function, used by data_manager_manual for instance
shed_conf_dict = self.get_shed_config_dict(app)
tool_path = None
relative_path = None
if shed_conf_dict:
tool_path = shed_conf_dict['tool_path']
relative_path = os.path.join(self.tool_shed_path_name, 'repos', self.owner, self.name, self.installed_changeset_revision)
return tool_path, relative_path
[docs] def guess_shed_config(self, app):
tool_ids = []
for tool in self.metadata.get('tools', []):
tool_ids.append(tool.get('guid'))
for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
name = shed_tool_conf_dict['config_filename']
for elem in shed_tool_conf_dict['config_elems']:
if elem.tag == 'tool':
for sub_elem in elem.findall('id'):
tool_id = sub_elem.text.strip()
if tool_id in tool_ids:
self.shed_config_filename = name
return shed_tool_conf_dict
elif elem.tag == "section":
for tool_elem in elem.findall('tool'):
for sub_elem in tool_elem.findall('id'):
tool_id = sub_elem.text.strip()
if tool_id in tool_ids:
self.shed_config_filename = name
return shed_tool_conf_dict
# We need to search by file paths here, which is less desirable.
tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url(self.tool_shed)
for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
tool_path = shed_tool_conf_dict['tool_path']
relative_path = os.path.join(tool_path, tool_shed, 'repos', self.owner, self.name)
if os.path.exists(relative_path):
self.shed_config_filename = shed_tool_conf_dict['config_filename']
return shed_tool_conf_dict
# Very last resort, get default shed_tool_config file for this instance
shed_tool_conf_dict = app.toolbox.default_shed_tool_conf_dict()
self.shed_config_filename = shed_tool_conf_dict['config_filename']
return shed_tool_conf_dict
@property
def has_readme_files(self):
return 'readme_files' in self.metadata
@property
def has_repository_dependencies(self):
repository_dependencies_dict = self.metadata.get('repository_dependencies', {})
repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
# [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]]
for rd_tup in repository_dependencies:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple(rd_tup)
if not asbool(only_if_compiling_contained_td):
return True
return False
@property
def has_repository_dependencies_only_if_compiling_contained_td(self):
repository_dependencies_dict = self.metadata.get('repository_dependencies', {})
repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
# [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]]
for rd_tup in repository_dependencies:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple(rd_tup)
if not asbool(only_if_compiling_contained_td):
return False
return True
@property
def in_error_state(self):
return self.status == self.installation_status.ERROR
@property
def includes_data_managers(self):
return bool(len(self.metadata.get('data_manager', {}).get('data_managers', {})))
@property
def includes_tools(self):
return 'tools' in self.metadata
@property
def includes_tools_for_display_in_tool_panel(self):
if self.includes_tools:
tool_dicts = self.metadata['tools']
for tool_dict in tool_dicts:
if tool_dict.get('add_to_tool_panel', True):
return True
return False
@property
def includes_tool_dependencies(self):
return 'tool_dependencies' in self.metadata
@property
def includes_workflows(self):
return 'workflows' in self.metadata
@property
def installed_repository_dependencies(self):
"""Return the repository's repository dependencies that are currently installed."""
installed_required_repositories = []
for required_repository in self.repository_dependencies:
if required_repository.status == self.installation_status.INSTALLED:
installed_required_repositories.append(required_repository)
return installed_required_repositories
@property
def installed_tool_dependencies(self):
"""Return the repository's tool dependencies that are currently installed, but possibly in an error state."""
installed_dependencies = []
for tool_dependency in self.tool_dependencies:
if tool_dependency.status in [ToolDependency.installation_status.INSTALLED]:
installed_dependencies.append(tool_dependency)
return installed_dependencies
@property
def is_deprecated_in_tool_shed(self):
if self.tool_shed_status:
return asbool(self.tool_shed_status.get('repository_deprecated', False))
return False
@property
def is_deactivated_or_installed(self):
return self.status in [self.installation_status.DEACTIVATED,
self.installation_status.INSTALLED]
@property
def is_installed(self):
return self.status == self.installation_status.INSTALLED
@property
def is_latest_installable_revision(self):
if self.tool_shed_status:
return asbool(self.tool_shed_status.get('latest_installable_revision', False))
return False
@property
def is_new(self):
return self.status == self.installation_status.NEW
@property
def missing_repository_dependencies(self):
"""Return the repository's repository dependencies that are not currently installed, and may not ever have been installed."""
missing_required_repositories = []
for required_repository in self.repository_dependencies:
if required_repository.status not in [self.installation_status.INSTALLED]:
missing_required_repositories.append(required_repository)
return missing_required_repositories
@property
def missing_tool_dependencies(self):
"""Return the repository's tool dependencies that are not currently installed, and may not ever have been installed."""
missing_dependencies = []
for tool_dependency in self.tool_dependencies:
if tool_dependency.status not in [ToolDependency.installation_status.INSTALLED]:
missing_dependencies.append(tool_dependency)
return missing_dependencies
[docs] def repo_files_directory(self, app):
repo_path = self.repo_path(app)
if repo_path:
return os.path.join(repo_path, self.name)
return None
[docs] def repo_path(self, app):
tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url(self.tool_shed)
for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
tool_path = shed_tool_conf_dict['tool_path']
relative_path = os.path.join(tool_path, tool_shed, 'repos', self.owner, self.name, self.installed_changeset_revision)
if os.path.exists(relative_path):
return relative_path
return None
@property
def repository_dependencies(self):
"""
Return all of this repository's repository dependencies, ignoring their attributes like prior_installation_required and
only_if_compiling_contained_td.
"""
required_repositories = []
for rrda in self.required_repositories:
repository_dependency = rrda.repository_dependency
required_repository = repository_dependency.repository
if required_repository:
required_repositories.append(required_repository)
return required_repositories
@property
def repository_dependencies_being_installed(self):
"""Return the repository's repository dependencies that are currently being installed."""
required_repositories_being_installed = []
for required_repository in self.repository_dependencies:
if required_repository.status in [self.installation_status.CLONING,
self.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
self.installation_status.INSTALLING_TOOL_DEPENDENCIES,
self.installation_status.LOADING_PROPRIETARY_DATATYPES,
self.installation_status.SETTING_TOOL_VERSIONS]:
required_repositories_being_installed.append(required_repository)
return required_repositories_being_installed
@property
def repository_dependencies_missing_or_being_installed(self):
"""Return the repository's repository dependencies that are either missing or currently being installed."""
required_repositories_missing_or_being_installed = []
for required_repository in self.repository_dependencies:
if required_repository.status in [self.installation_status.ERROR,
self.installation_status.INSTALLING,
self.installation_status.NEVER_INSTALLED,
self.installation_status.UNINSTALLED]:
required_repositories_missing_or_being_installed.append(required_repository)
return required_repositories_missing_or_being_installed
@property
def repository_dependencies_with_installation_errors(self):
"""Return the repository's repository dependencies that have installation errors."""
required_repositories_with_installation_errors = []
for required_repository in self.repository_dependencies:
if required_repository.status == self.installation_status.ERROR:
required_repositories_with_installation_errors.append(required_repository)
return required_repositories_with_installation_errors
@property
def requires_prior_installation_of(self):
"""
Return a list of repository dependency tuples like (tool_shed, name, owner, changeset_revision, prior_installation_required) for this
repository's repository dependencies where prior_installation_required is True. By definition, repository dependencies are required to
be installed in order for this repository to function correctly. However, those repository dependencies that are defined for this
repository with prior_installation_required set to True place them in a special category in that the required repositories must be
installed before this repository is installed. Among other things, this enables these "special" repository dependencies to include
information that enables the successful installation of this repository. This method is not used during the initial installation of
this repository, but only after it has been installed (metadata must be set for this repository in order for this method to be useful).
"""
required_rd_tups_that_must_be_installed = []
if self.has_repository_dependencies:
rd_tups = self.metadata['repository_dependencies']['repository_dependencies']
for rd_tup in rd_tups:
if len(rd_tup) == 5:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple(rd_tup, contains_error=False)
if asbool(prior_installation_required):
required_rd_tups_that_must_be_installed.append((tool_shed, name, owner, changeset_revision, 'True', 'False'))
elif len(rd_tup) == 6:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple(rd_tup, contains_error=False)
# The repository dependency will only be required to be previously installed if it does not fall into the category of
# a repository that must be installed only so that its contained tool dependency can be used for compiling the tool
# dependency of the dependent repository.
if not asbool(only_if_compiling_contained_td):
if asbool(prior_installation_required):
required_rd_tups_that_must_be_installed.append((tool_shed, name, owner, changeset_revision, 'True', 'False'))
return required_rd_tups_that_must_be_installed
@property
def revision_update_available(self):
# This method should be named update_available, but since it is no longer possible to drop a table column using migration scripts
# with the sqlite database (see ~/galaxy/model/migrate/versions/0016_drop_update_available_col_add_tool_shed_status_col.py), we
# have to name it in such a way that it will not conflict with the eliminated tool_shed_repository.update_available column (which
# cannot be eliminated if using the sqlite database).
if self.tool_shed_status:
return asbool(self.tool_shed_status.get('revision_update', False))
return False
[docs] def to_dict(self, view='collection', value_mapper=None):
if value_mapper is None:
value_mapper = {}
rval = {}
try:
visible_keys = self.__getattribute__(f"dict_{view}_visible_keys")
except AttributeError:
raise Exception(f'Unknown API view: {view}')
for key in visible_keys:
try:
rval[key] = self.__getattribute__(key)
if key in value_mapper:
rval[key] = value_mapper.get(key, rval[key])
except AttributeError:
rval[key] = None
return rval
@property
def tool_dependencies_being_installed(self):
dependencies_being_installed = []
for tool_dependency in self.tool_dependencies:
if tool_dependency.status == ToolDependency.installation_status.INSTALLING:
dependencies_being_installed.append(tool_dependency)
return dependencies_being_installed
@property
def tool_dependencies_installed_or_in_error(self):
"""Return the repository's tool dependencies that are currently installed, but possibly in an error state."""
installed_dependencies = []
for tool_dependency in self.tool_dependencies:
if tool_dependency.status in [ToolDependency.installation_status.INSTALLED,
ToolDependency.installation_status.ERROR]:
installed_dependencies.append(tool_dependency)
return installed_dependencies
@property
def tool_dependencies_missing_or_being_installed(self):
dependencies_missing_or_being_installed = []
for tool_dependency in self.tool_dependencies:
if tool_dependency.status in [ToolDependency.installation_status.ERROR,
ToolDependency.installation_status.INSTALLING,
ToolDependency.installation_status.NEVER_INSTALLED,
ToolDependency.installation_status.UNINSTALLED]:
dependencies_missing_or_being_installed.append(tool_dependency)
return dependencies_missing_or_being_installed
@property
def tool_dependencies_with_installation_errors(self):
dependencies_with_installation_errors = []
for tool_dependency in self.tool_dependencies:
if tool_dependency.status == ToolDependency.installation_status.ERROR:
dependencies_with_installation_errors.append(tool_dependency)
return dependencies_with_installation_errors
@property
def tool_shed_path_name(self):
tool_shed_url = self.tool_shed
if tool_shed_url.find(':') > 0:
# Eliminate the port, if any, since it will result in an invalid directory name.
tool_shed_url = tool_shed_url.split(':')[0]
return tool_shed_url.rstrip('/')
@property
def tuples_of_repository_dependencies_needed_for_compiling_td(self):
"""
Return tuples defining this repository's repository dependencies that are necessary only for compiling this repository's tool
dependencies.
"""
rd_tups_of_repositories_needed_for_compiling_td = []
repository_dependencies = self.metadata.get('repository_dependencies', {})
rd_tups = repository_dependencies.get('repository_dependencies', [])
for rd_tup in rd_tups:
if len(rd_tup) == 6:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup
if asbool(only_if_compiling_contained_td):
rd_tups_of_repositories_needed_for_compiling_td.append((tool_shed, name, owner, changeset_revision, 'False', 'True'))
return rd_tups_of_repositories_needed_for_compiling_td
@property
def uninstalled_repository_dependencies(self):
"""Return the repository's repository dependencies that have been uninstalled."""
uninstalled_required_repositories = []
for required_repository in self.repository_dependencies:
if required_repository.status == self.installation_status.UNINSTALLED:
uninstalled_required_repositories.append(required_repository)
return uninstalled_required_repositories
@property
def uninstalled_tool_dependencies(self):
"""Return the repository's tool dependencies that have been uninstalled."""
uninstalled_tool_dependencies = []
for tool_dependency in self.tool_dependencies:
if tool_dependency.status == ToolDependency.installation_status.UNINSTALLED:
uninstalled_tool_dependencies.append(tool_dependency)
return uninstalled_tool_dependencies
@property
def upgrade_available(self):
if self.tool_shed_status:
if self.is_deprecated_in_tool_shed:
# Only allow revision upgrades if the repository is not deprecated in the tool shed.
return False
return asbool(self.tool_shed_status.get('revision_upgrade', False))
return False
[docs]class RepositoryRepositoryDependencyAssociation(_HasTable):
def __init__(self, tool_shed_repository_id=None, repository_dependency_id=None):
self.tool_shed_repository_id = tool_shed_repository_id
self.repository_dependency_id = repository_dependency_id
[docs]class RepositoryDependency(_HasTable):
def __init__(self, tool_shed_repository_id=None):
self.tool_shed_repository_id = tool_shed_repository_id
[docs]class ToolDependency(_HasTable):
# converting this one to Enum breaks the tool shed tests,
# don't know why though -John
installation_status = Bunch(NEVER_INSTALLED='Never installed',
INSTALLING='Installing',
INSTALLED='Installed',
ERROR='Error',
UNINSTALLED='Uninstalled')
[docs] class states(str, Enum):
INSTALLING = 'running'
OK = 'ok'
WARNING = 'queued'
ERROR = 'error'
UNINSTALLED = 'deleted_new'
def __init__(self, tool_shed_repository_id=None, name=None, version=None, type=None, status=None, error_message=None):
self.tool_shed_repository_id = tool_shed_repository_id
self.name = name
self.version = version
self.type = type
self.status = status
self.error_message = error_message
@property
def can_install(self):
return self.status in [self.installation_status.NEVER_INSTALLED, self.installation_status.UNINSTALLED]
@property
def can_uninstall(self):
return self.status in [self.installation_status.ERROR, self.installation_status.INSTALLED]
@property
def can_update(self):
return self.status in [self.installation_status.NEVER_INSTALLED,
self.installation_status.INSTALLED,
self.installation_status.ERROR,
self.installation_status.UNINSTALLED]
[docs] def get_env_shell_file_path(self, app):
installation_directory = self.installation_directory(app)
file_path = os.path.join(installation_directory, 'env.sh')
if os.path.exists(file_path):
return file_path
return None
@property
def in_error_state(self):
return self.status == self.installation_status.ERROR
[docs] def installation_directory(self, app):
if self.type == 'package':
return os.path.join(app.tool_dependency_dir,
self.name,
self.version,
self.tool_shed_repository.owner,
self.tool_shed_repository.name,
self.tool_shed_repository.installed_changeset_revision)
if self.type == 'set_environment':
return os.path.join(app.tool_dependency_dir,
'environment_settings',
self.name,
self.tool_shed_repository.owner,
self.tool_shed_repository.name,
self.tool_shed_repository.installed_changeset_revision)
@property
def is_installed(self):
return self.status == self.installation_status.INSTALLED
[docs]class ToolVersion(Dictifiable, _HasTable):
dict_element_visible_keys = ['id', 'tool_shed_repository']
def __init__(self, id=None, create_time=None, tool_id=None, tool_shed_repository=None):
self.id = id
self.create_time = create_time
self.tool_id = tool_id
self.tool_shed_repository = tool_shed_repository
[docs] def to_dict(self, view='element'):
rval = super().to_dict(view=view)
rval['tool_name'] = self.tool_id
for a in self.parent_tool_association:
rval['parent_tool_id'] = a.parent_id
for a in self.child_tool_association:
rval['child_tool_id'] = a.tool_id
return rval
[docs]class ToolVersionAssociation(_HasTable):
def __init__(self, id=None, tool_id=None, parent_id=None):
self.id = id
self.tool_id = tool_id
self.parent_id = parent_id